[English] 日本語
Yorodumi- PDB-6i3i: Crystal structure of reactive center loop (RCL) cleaved angiotens... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i3i | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of reactive center loop (RCL) cleaved angiotensinogen | ||||||||||||
Components | Angiotensinogen | ||||||||||||
Keywords | HORMONE / angiotensinogen / reactive center loop | ||||||||||||
Function / homology | Function and homology information regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / regulation of renal sodium excretion / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / : / regulation of extracellular matrix assembly / regulation of renal output by angiotensin / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger ...regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / regulation of renal sodium excretion / maintenance of blood vessel diameter homeostasis by renin-angiotensin / negative regulation of neurotrophin TRK receptor signaling pathway / : / regulation of extracellular matrix assembly / regulation of renal output by angiotensin / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / renin-angiotensin regulation of aldosterone production / renal system process / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of macrophage derived foam cell differentiation / positive regulation of extracellular matrix assembly / positive regulation of CoA-transferase activity / vasoconstriction / low-density lipoprotein particle remodeling / type 1 angiotensin receptor binding / positive regulation of extrinsic apoptotic signaling pathway / response to angiotensin / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of cardiac muscle hypertrophy / positive regulation of protein tyrosine kinase activity / positive regulation of gap junction assembly / regulation of cardiac conduction / regulation of vasoconstriction / blood vessel remodeling / Metabolism of Angiotensinogen to Angiotensins / positive regulation of epithelial to mesenchymal transition / nitric oxide-cGMP-mediated signaling / negative regulation of MAP kinase activity / positive regulation of protein metabolic process / positive regulation of endothelial cell migration / Peptide ligand-binding receptors / kidney development / positive regulation of cytokine production / angiotensin-activated signaling pathway / regulation of cell growth / growth factor activity / serine-type endopeptidase inhibitor activity / hormone activity / PPARA activates gene expression / regulation of blood pressure / positive regulation of miRNA transcription / positive regulation of inflammatory response / positive regulation of reactive oxygen species metabolic process / positive regulation of fibroblast proliferation / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / G alpha (q) signalling events / collagen-containing extracellular matrix / regulation of apoptotic process / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / positive regulation of DNA-templated transcription / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å | ||||||||||||
Authors | Yan, Y. / Read, R.J. | ||||||||||||
Funding support | United Kingdom, 3items
| ||||||||||||
Citation | Journal: J. Biol. Chem. / Year: 2019 Title: Structural basis for the specificity of renin-mediated angiotensinogen cleavage. Authors: Yan, Y. / Zhou, A. / Carrell, R.W. / Read, R.J. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6i3i.cif.gz | 96.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6i3i.ent.gz | 72.7 KB | Display | PDB format |
PDBx/mmJSON format | 6i3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i3i_validation.pdf.gz | 447.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6i3i_full_validation.pdf.gz | 448.5 KB | Display | |
Data in XML | 6i3i_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 6i3i_validation.cif.gz | 20.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/6i3i ftp://data.pdbj.org/pub/pdb/validation_reports/i3/6i3i | HTTPS FTP |
-Related structure data
Related structure data | 5m3xC 5m3yC 6i3fC 2wxwS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 50647.656 Da / Num. of mol.: 1 / Mutation: N137Q,N271Q,N295Q,C232S,C308S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGT, SERPINA8 / Plasmid: pCEP4 / Cell (production host): HEK293EBNA / Production host: Homo sapiens (human) / References: UniProt: P01019 |
---|---|
#2: Sugar | ChemComp-NAG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.36 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.5M ammonium sulfate, 0.1M Tris pH8.5 12% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→66.14 Å / Num. obs: 15316 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.987 / Rmerge(I) obs: 0.214 / Rrim(I) all: 0.254 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.97→3.05 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.282 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1106 / CC1/2: 0.53 / Rrim(I) all: 1.505 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2wxw Resolution: 2.97→66.14 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.916 / SU B: 18.186 / SU ML: 0.313 / Cross valid method: THROUGHOUT / ESU R: 1.089 / ESU R Free: 0.343 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.732 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.97→66.14 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|